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Aliases for HOXA4 Gene

Aliases for HOXA4 Gene

  • Homeobox A4 2 3 5
  • Homeobox Protein Hox-1.4 3 4
  • Homeobox Protein Hox-1D 3 4
  • Homeo Box A4 2 3
  • HOX1D 3 4
  • Homeobox Protein Hox-A4 3
  • Hox-1.4-Like Protein 3
  • Dfd-Like Protein 3
  • HOX1 3

External Ids for HOXA4 Gene

Previous HGNC Symbols for HOXA4 Gene

  • HOX1D
  • HOX1

Previous GeneCards Identifiers for HOXA4 Gene

  • GC07M026810
  • GC07M026911
  • GC07M026912
  • GC07M026941
  • GC07M027134
  • GC07M027048
  • GC07M027170

Summaries for HOXA4 Gene

Entrez Gene Summary for HOXA4 Gene

  • In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. [provided by RefSeq, Jul 2008]

GeneCards Summary for HOXA4 Gene

HOXA4 (Homeobox A4) is a Protein Coding gene. Diseases associated with HOXA4 include Hypospadias. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Developmental Biology. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and sequence-specific DNA binding. An important paralog of this gene is HOXD4.

UniProtKB/Swiss-Prot for HOXA4 Gene

  • Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Binds to sites in the 5-flanking sequence of its coding region with various affinities. The consensus sequences of the high and low affinity binding sites are 5-TAATGA[CG]-3 and 5-CTAATTTT-3.

Gene Wiki entry for HOXA4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXA4 Gene

Genomics for HOXA4 Gene

Regulatory Elements for HOXA4 Gene

Enhancers for HOXA4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH07G026855 1.4 Ensembl ENCODE dbSUPER 12.2 +273.3 273252 4.8 HDAC1 PKNOX1 NFIB FEZF1 ZBTB40 TCF12 GLIS2 GATA2 EGR1 ZNF366 HOTAIRM1 HOXA5 HOXA-AS3 HOXA4 HOXA3 HOXA6 HOXA1 HOXA2 HOXA-AS2 SKAP2
GH07G026862 1.4 ENCODE dbSUPER 11.8 +266.7 266685 3.1 HDGF PKNOX1 CREB3L1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 HOTAIRM1 HOXA-AS3 HOXA4 HOXA3 HOXA6 HOXA5 HOXA1 HOXA2 HOXA10-AS HOXA9
GH07G027095 3.3 VISTA FANTOM5 Ensembl ENCODE dbSUPER 3.8 -7.4 -7397 86.3 MLX ZFP64 DMAP1 FEZF1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 HOTAIRM1 HOXA10-AS HOXA2 HOXA-AS2 HOXA9 HOXA11-AS HOXA10 HOXA11 EIF4HP1 SKAP2
GH07G026853 0.9 ENCODE dbSUPER 12 +276.8 276823 0.2 CTCF ZNF654 ZSCAN4 CHD1 BMI1 RAD21 PRDM6 SMC3 REPIN1 SP7 HOXA5 HOXA3 HOXA6 HOXA-AS3 HOXA4 HOTAIRM1 HOXA1 GC07P026846 RPL7AP38
GH07G026860 0.9 ENCODE dbSUPER 11.8 +270.3 270263 0.2 ELF3 CTCF ZNF654 JUND SMC3 RAD21 MIXL1 EZH2 HOXA-AS3 HOXA4 HOXA5 HOXA3 HOXA6 HOTAIRM1 HOXA1 HOXA2 HOXA-AS2 GC07P026846
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HOXA4 on UCSC Golden Path with GeneCards custom track

Promoters for HOXA4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000325314 99 1401 HDGF PKNOX1 MLX ARNT ARID4B SIN3A FEZF1 ZNF48 GLIS2 FOS
ENSR00000209832 1099 201 PKNOX1 GLI4 FEZF1 ZNF2 GLIS2 KLF7 SP3 ZNF488 REST ZNF623

Genomic Location for HOXA4 Gene

Chromosome:
7
Start:
27,128,507 bp from pter
End:
27,130,799 bp from pter
Size:
2,293 bases
Orientation:
Minus strand

Genomic View for HOXA4 Gene

Genes around HOXA4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXA4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXA4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXA4 Gene

Proteins for HOXA4 Gene

  • Protein details for HOXA4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q00056-HXA4_HUMAN
    Recommended name:
    Homeobox protein Hox-A4
    Protein Accession:
    Q00056
    Secondary Accessions:
    • A4D180
    • O43366

    Protein attributes for HOXA4 Gene

    Size:
    320 amino acids
    Molecular mass:
    34499 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HOXA4 Gene

Post-translational modifications for HOXA4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HOXA4 Gene

No data available for DME Specific Peptides for HOXA4 Gene

Domains & Families for HOXA4 Gene

Gene Families for HOXA4 Gene

Suggested Antigen Peptide Sequences for HOXA4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q00056

UniProtKB/Swiss-Prot:

HXA4_HUMAN :
  • Belongs to the Antp homeobox family. Deformed subfamily.
Family:
  • Belongs to the Antp homeobox family. Deformed subfamily.
genes like me logo Genes that share domains with HOXA4: view

Function for HOXA4 Gene

Molecular function for HOXA4 Gene

GENATLAS Biochemistry:
homeo box A4(1D),homologous to mouse Hox-1.4,Drosophila Dfd
UniProtKB/Swiss-Prot Function:
Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Binds to sites in the 5-flanking sequence of its coding region with various affinities. The consensus sequences of the high and low affinity binding sites are 5-TAATGA[CG]-3 and 5-CTAATTTT-3.

Gene Ontology (GO) - Molecular Function for HOXA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003700 transcription factor activity, sequence-specific DNA binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with HOXA4: view
genes like me logo Genes that share phenotypes with HOXA4: view

Animal Models for HOXA4 Gene

MGI Knock Outs for HOXA4:

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for HOXA4 Gene

Localization for HOXA4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXA4 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HOXA4 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for HOXA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0016604 nuclear body IDA --
genes like me logo Genes that share ontologies with HOXA4: view

Pathways & Interactions for HOXA4 Gene

genes like me logo Genes that share pathways with HOXA4: view

Gene Ontology (GO) - Biological Process for HOXA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IEA --
GO:0009653 anatomical structure morphogenesis TAS 1675427
genes like me logo Genes that share ontologies with HOXA4: view

No data available for SIGNOR curated interactions for HOXA4 Gene

Transcripts for HOXA4 Gene

mRNA/cDNA for HOXA4 Gene

Unigene Clusters for HOXA4 Gene

Homeobox A4:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for HOXA4 Gene

No ASD Table

Relevant External Links for HOXA4 Gene

GeneLoc Exon Structure for
HOXA4
ECgene alternative splicing isoforms for
HOXA4

Expression for HOXA4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HOXA4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXA4 Gene

This gene is overexpressed in Esophagus - Muscularis (x7.3) and Esophagus - Gastroesophageal Junction (x6.8).

Protein differential expression in normal tissues from HIPED for HOXA4 Gene

This gene is overexpressed in Neutrophil (23.8), Tlymphocyte (12.9), Nasal epithelium (10.8), and Blymphocyte (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for HOXA4 Gene



Protein tissue co-expression partners for HOXA4 Gene

NURSA nuclear receptor signaling pathways regulating expression of HOXA4 Gene:

HOXA4

SOURCE GeneReport for Unigene cluster for HOXA4 Gene:

Hs.533357

mRNA Expression by UniProt/SwissProt for HOXA4 Gene:

Q00056-HXA4_HUMAN
Tissue specificity: Embryonic nervous system.
genes like me logo Genes that share expression patterns with HOXA4: view

Primer Products

No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXA4 Gene

Orthologs for HOXA4 Gene

This gene was present in the common ancestor of animals.

Orthologs for HOXA4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HOXA4 34 35
  • 99.37 (n)
dog
(Canis familiaris)
Mammalia HOXA4 34 35
  • 91.59 (n)
cow
(Bos Taurus)
Mammalia HOXA4 34 35
  • 90.22 (n)
rat
(Rattus norvegicus)
Mammalia LOC100360577 34
  • 83.99 (n)
mouse
(Mus musculus)
Mammalia Hoxa4 34 16 35
  • 83.27 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia HOXA4 35
  • 66 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia HOXA4 35
  • 55 (a)
OneToOne
chicken
(Gallus gallus)
Aves LOC100858429 34
  • 94.44 (n)
HOXA4 35 35
  • 60 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia HOXA4 35
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxa4 34
  • 66.67 (n)
fruit fly
(Drosophila melanogaster)
Insecta Dfd 36 35
  • 73 (a)
Scr 36
  • 60 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 28 (a)
OneToMany
Species where no ortholog for HOXA4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for HOXA4 Gene

ENSEMBL:
Gene Tree for HOXA4 (if available)
TreeFam:
Gene Tree for HOXA4 (if available)

Paralogs for HOXA4 Gene

Variants for HOXA4 Gene

Sequence variations from dbSNP and Humsavar for HOXA4 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
VAR_036266 A breast cancer sample
rs1001379085 -- 27,128,387(+) AATTA(A/T)GTGAG intron-variant, nc-transcript-variant, downstream-variant-500B, upstream-variant-2KB
rs1001544497 -- 27,128,830(+) AGGTA(A/G)GGAAG intron-variant, downstream-variant-500B, upstream-variant-2KB, utr-variant-3-prime
rs1002143143 -- 27,128,852(+) GTCTG(A/T)CTTCT intron-variant, downstream-variant-500B, upstream-variant-2KB, utr-variant-3-prime
rs1002822603 -- 27,132,201(+) GGCAT(G/T)CAAAA intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for HOXA4 Gene

Variant ID Type Subtype PubMed ID
dgv1094n67 CNV gain 20364138
dgv11244n54 CNV loss 21841781
nsv5674 CNV deletion 18451855
nsv606464 CNV loss 21841781
nsv606465 CNV loss 21841781
nsv7393 OTHER inversion 18451855
nsv824042 CNV gain 20364138

Variation tolerance for HOXA4 Gene

Residual Variation Intolerance Score: 73.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.09; 80.48% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HOXA4 Gene

Human Gene Mutation Database (HGMD)
HOXA4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HOXA4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXA4 Gene

Disorders for HOXA4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for HOXA4 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
hypospadias
  • familial hypospadias
- elite association - COSMIC cancer census association via MalaCards
Search HOXA4 in MalaCards View complete list of genes associated with diseases

Relevant External Links for HOXA4

Genetic Association Database (GAD)
HOXA4
Human Genome Epidemiology (HuGE) Navigator
HOXA4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HOXA4
genes like me logo Genes that share disorders with HOXA4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HOXA4 Gene

Publications for HOXA4 Gene

  1. High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men. (PMID: 19453261) Yerges L.M. … Zmuda J.M. (J. Bone Miner. Res. 2009) 3 46 64
  2. Mutation screening of BMP4, BMP7, HOXA4 and HOXB6 genes in Chinese patients with hypospadias. (PMID: 17003840) Chen T. … Shen Y. (Eur. J. Hum. Genet. 2007) 3 46 64
  3. The DNA sequence of human chromosome 7. (PMID: 12853948) Hillier L.W. … Wilson R.K. (Nature 2003) 3 4 64
  4. Vertebrate homeobox gene nomenclature. (PMID: 1358459) Scott M.P. (Cell 1992) 2 3 64
  5. Alteration of homeobox gene expression by N-ras transformation of PA- 1 human teratocarcinoma cells. (PMID: 1675427) Buettner R. … Tainsky M.A. (Mol. Cell. Biol. 1991) 3 4 64

Products for HOXA4 Gene

Sources for HOXA4 Gene

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